Having trouble joining two edges
Don't use the fill tool. Delete that big and ugly n-gon shown in the pictures, then select the edge loops you want to join (&#9095; Alt+ RMB), and press the space bar and type Bridge Edge loops



Read: How to connect vertices in a mesh efficiently?. 

Then, if you are using a subsurf modifier you need to select the edges you want to make sharp and crease them. Press &#8679; Shift+E and set the edge crease to a valud of 1.0

read: Keep sharp edges when using subdivision surface